Mihály Váradi

R2DT: a comprehensive platform for visualising RNA secondary structure

R2DT is a software platform for visualizing RNA secondary structures with enhanced features like SNP display and template-free visualization.

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank

The PDB NextGen Archive centralizes and streamlines access to integrated structural annotations and enriched data from wwPDB partners and external sources.

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank

PDBe CCDUtils processes and analyzes small molecules from the PDB using RDKit, offering tools for property computation and database cross-references.

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

The paper standardizes naming and annotations for macromolecular complexes in the PDB using external resources, improving FAIRness and enabling better research and education.

Clustering predicted structures at the scale of the known protein universe

A Foldseek-based linear-time structural clustering groups 52 million AlphaFold DB representatives into 2.27 million non-singleton clusters; 31% lack known structural or domain annotation.

Identifying Protein Conformational States in the PDB and Comparison to AlphaFold2 Predictions

The paper clusters experimentally determined protein structures to identify conformational states and compares them to AlphaFold2 predictions.

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models

ModelCIF extends the PDBx/mmCIF standard to represent predicted 3D protein models, enabling FAIR data sharing for computational structural biology.

Unified access to up-to-date residue-level annotations from UniProt and other biological databases for PDB data via PDBx/mmCIF files

The paper integrates up-to-date residue-level annotations from multiple databases into PDBx/mmCIF files to improve data interoperability and standardization.

Comprehensive collection and prediction of ABC transmembrane protein structures in the AI era of structural biology

The paper collects and predicts structures of ABC transmembrane proteins using AlphaFold2 and presents them via a web application.

PDB ProtVista: A reusable and open-source sequence feature viewer

PDB ProtVista is a sequence feature viewer that provides 2D visualization of residue-level annotations and integrates with 3D molecular viewers.

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

3D-Beacons provides a federated network to unify access to protein structure data from multiple sources, enabling comparative analysis of models.